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<h1>Calculator Plugins</h1>

<h2><a name="chargegroup"></a>Charge</h2>

<h3><a name="charge"></a>Charge Plugin</h3>
<p>The partial charge distribution determines many physico-chemical
properties of a molecule, such as ionization constants, reactivity and
pharmacophore pattern. Use Charge plugin to compute the partial charge
value of each atom. Total charge is calculated from sigma and pi charge
components, and any of these three charge values can be displayed. You can change 
between these by setting the "Type" option in the <b CLASS="buttonName">Charge Options</b> 
panel; by default, the total charge is displayed. You can also <BR>
<a href="charge.html">Learn more</a> about how the plugin calculates the
partial charge.</p>
<p>
<table>
	<tr>
		<td><img src="images/charge.png" width="563" height="370"></td>
	</tr>
</table>
</p>
<p>The numbers in brackets refer to the charge sums of implicit H
atoms, and displayed only if the "Increment of Hs" option is switched on 
in the <b>Charge Options</b> panel.</p>
<p>
<table>
	<tr>
		<td><img src="images/charge_mspace.png" width="733" height="602"></td>
	</tr>
</table>
</p>

<h3><a name="polarizability"></a>Polarizability Plugin</h3>
<p>The electric field generated by partial charges of a molecule
spread through intermolecular cavities and the solvent that the molecule
is solved within. The induced partial charge (induced dipole) has a
tendency to diminish the external electric field. This phenomenon is
called as polarizability. The more stable each ionized site is the more
its vicinity is polarizable. This is why atomic polarizability is an
important factor in the determination of p<i>K</i><sub>a</sub> and why
it is considered in our p<i>K</i><sub>a</sub> calculation plugin. Atomic
polarizability is altered by partial charges of atoms. Our calculation
is based on <a HREF="#ref3">Ref.3.</a>, and takes into account the
effect of partial charge upon atomic polarizability.</p>
<p>
<table cellpadding="4">
	<tr>
		<td><img src="images/polarizability.png" width="388" height="429"></td>
		<td><img src="images/polarizability_mspace.png" width="808" height="430"></td>
	</tr>
</table>
</p>

<h3><a name="oen"></a>Orbital Electronegativity Plugin</h3>
<p>Partial charge distribution of the molecule is governed by the
orbital electronegativity of the atoms contained in the molecule.<BR> 
<a href="charge.html#Concept of Orbital Electronegativity">Learn more</a> about how the plugin calculates
orbital electronegativity.</p>
<p>
<table>
	<tr>
		<td><img src="images/oen.png" width="388" height="407"></td>
	</tr>
</table>
</p>